Bacterial and Virus Strains |
|
One Shot TOP10 Chemically Competent E. coli
|
Invitrogen |
C404006 |
|
Chemicals, Peptides and Recombinant Proteins |
|
Tricaine (MS-222) |
Syndel |
Tricaine-S |
SU5402 |
Selleckchem |
S7667 |
Nicotinamide (NAM) |
Sigma |
N0636 |
Sirtinol |
Sigma |
566321 |
FK-866 |
Cayman Chemical |
13287 |
Doxycycline |
Sigma |
D9891 |
Cas9 protein |
PNA Bio |
CP01-200 |
T7 nuclease |
New England Biolabs |
M0302L |
Pfusion Taq polymerase |
New England Biolabs |
M0535L |
|
Critical Commercial Assays |
|
mMESSAGE mMACHINE |
Invitrogen |
AM1340 |
MEGAshortscript Kit |
ThermoFisher SCIENTIFIC |
AM1354 |
RNeasy Mini Kit |
QIAGEN |
74104 |
Superscript VILO cDNA Synthesis Kit |
Invitrogen |
11754050 |
LightCycler 480 SYBR Green master mix |
Roche |
04-887-352-001 |
TruSeq RNA Library Prep Kit v2 |
Illumina |
RS-122-2001 |
Gateway LR Clonase II Enzyme mix |
ThermoFisher SCIENTIFIC |
11791020 |
Trizol Reagent |
ThermoFisher SCIENTIFIC |
15596018 |
|
Deposited Data |
|
Raw and analyzed data |
This paper |
GEO:GSE182113
|
|
Experimental Models: Organisms/Strains |
|
Zebrafish hspd1 mutant strain (nbl) |
ZIRC |
ZL737 |
Zebrafish strain sirt1wcm18/wcm18
|
This paper |
sirt1wcm18/wcm18
|
Zebrafish strain sirt1wcm19/wcm19
|
This paper |
sirt1wcm19/wcm19
|
Zebrafish strain Tg(hspd1:d2-gfp)wcm20
|
This paper |
Tg(hspd1:d2-gfp)wcm20
|
|
Oligonucleotides |
|
PCR primer sequences |
IDT |
See Table S1
|
sirt1 mutant genotyping primers |
IDT |
See Table S1
|
hspd1 promoter cloning primers |
IDT |
See Table S1
|
Mouse ODC D2 fragment cloning primers |
IDT |
See Table S1
|
sirt1 gRNA for CRISPR-Cas9 mutagenesis |
IDT |
See Table S1
|
|
Recombinant DNA |
|
pCR4Blunt-TOPO |
ThermoFisher SCIENTIFIC |
K287520 |
pDestTol2pA2 |
Addgene |
http://tol2kit.genetics.utah.edu |
p5E-MCS |
Addgene |
http://tol2kit.genetics.utah.edu |
pCS2FA-transposase |
Addgene |
http://tol2kit.genetics.utah.edu |
pME-EGFP |
Addgene |
http://tol2kit.genetics.utah.edu |
|
Software and Algorithms |
|
ImageJ |
NIH |
https://imagej.nih.gov/ij/ |
R |
Cran |
https://www.R-project.org/ |
Star V2.3 |
rna-star |
http://code.google.com/p/rna-star/ |
DESeq2 |
Bioconductor |
https://doi.org/10.18129/B9.bioc.DESeq2 |
Prism7 |
Graphpad |
https://www.graphpad.com/scientific-software/prism/ |
GSEA |
UC-SanDiego, Broad Institute |
https://www.gsea-msigdb.org/gsea/ |